Bevel Tool not cutting evenly
You have a couple of coincident edges.

If you start with an edge close to the corner, the bevel will be clamped on one side (left and middle, below). If the edge is slid all the way down so you can't see it, the bevel will only happen on one side (right).



Note, if you're in Face selection mode, and you have face markers switched on, you can see the scrunched face .. it's the dot in the middle of the corner edge. 

Solution: Remove doubles (2.79: CtrlV,R. 2.8: AltM Merge > 'By Distance')